To uncover mechanism of highly weakened carbon metabolism in chlorotic tea ( Camellia sinensis) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in the tea plant cultivar “Huangjinya”. A total of 2110 proteins were identified in “Huangjinya”, and 173 proteins showed differential accumulations between the chlorotic and normal green leaves. Of these, 19 proteins were correlated with RNA expression levels, based on integrated analyses of the transcriptome and proteome. Moreover, the results of our analysis of differentially expressed proteins suggested that primary carbon metabolism (i.e., carbohydrate synthesis and transport) was inhibited in chlorotic tea leaves. The differentially expressed genes and proteins combined with photosynthetic phenotypic data indicated that 4-coumarate-CoA ligase (4CL) showed a major effect on repressing flavonoid metabolism, and abnormal developmental chloroplast inhibited the accumulation of chlorophyll and flavonoids because few carbon skeletons were provided as a result of a weakened primary carbon metabolism. Additionally, a positive feedback mechanism was verified at the protein level (Mg chelatase and chlorophyll b reductase) in the chlorophyll biosynthetic pathway, which might effectively promote the accumulation of chlorophyll b in response to the demand for this pigment in the cells of chlorotic tea leaves in weakened carbon metabolism.